The Red Sea is a harsh environment characterized by high salinity and temperature, and how benthic organisms respond to the environment therein is still relatively unexplored. Here, we looked at the intertidal population of the snake sea cucumber, Synapta maculata, found in a species-rich seagrass meadow on the southern coast of the Red Sea in Saudi Arabia. The objectives of the study were (1) to examine the changes in S. maculata abundance from spring to fall in a multi-species seagrass meadow (Halodule pinifolia, Halodule univervis, Halophila ovalis, and Halophila stipulacea) and (2) to determine the relationship between the abundance of S. maculata with the selected abiotic environmental variables (depth, salinity, temperature, pH, dissolved oxygen, wind speed, wind direction, air temperature, relative humidity, and barometric pressure). The abundance of S. maculata was assessed using three permanent 50 × 4 m belt transects. Results showed that the abundance of S. maculata was present from March to June (approximately 4 individuals per 200 m2). We observed a drastic decline in the following months that coincided with the die-off of the seagrass meadow. The abundance of S. maculata differed significantly among sampling months. Correlation analysis revealed a significant positive relationship between the abundance of S. maculata and dissolved oxygen, wind speed, and barometric pressure. At the same time, salinity, water temperature, and air temperature showed a significant negative relationship. The generalized linear model suggested salinity, pH, and dissolved oxygen were the main environmental factors that influence the population of S. maculata. Overall, the population dynamics of S. maculata in this area was driven by the combination of extreme abiotic environmental factors and the presence of seagrass meadows.